[gmx-users] Re: equilibrium stage runs for too long

Justin Lemkul jalemkul at vt.edu
Thu Aug 23 21:15:50 CEST 2012

On 8/23/12 2:37 PM, Clare wrote:
> Hi Justin,
> Thank you so much for your reply!
> what could be the fundamental things that went wrong? for example, is it the
> problem of the parameters I used in my mdp file or the problem in the system
> itself?

Either, both, or neither.  Slow run times are generally incorrect .mdp 
parameters (which you haven't shown), incorrect use of mdrun (you haven't shown 
your command), or some problem external to Gromacs (MPI/threading environment, 
hardware, etc).

> The way I built my system is that, firstly I created three boxes containing
> water, lipid and decane respectively using random insertion, and I performed
> EM,NVT and NPT on each box. After this, I built a new box and placed the
> three boxes in it one by one, and finally EM was performed on this big box.
> The result from EM was:
> Steepest Descents converged to Fmax < 1000 in 168 steps
> Potential Energy  = -4.7134688e+05
> Maximum force     =  8.5041827e+02 on atom 634
> Norm of force     =  4.4439018e+01
> Does that show any clue?

None of that indicates anything that would give rise to the problem at hand. 
Your EM appears entirely normal.



Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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